Multiple sequence alignment - TraesCS2A01G231600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G231600 chr2A 100.000 4007 0 0 1 4007 271913178 271909172 0.000000e+00 7400.0
1 TraesCS2A01G231600 chr2B 92.702 1658 39 28 776 2387 296003621 296005242 0.000000e+00 2316.0
2 TraesCS2A01G231600 chr2B 93.151 1095 36 17 2925 4007 296012709 296013776 0.000000e+00 1570.0
3 TraesCS2A01G231600 chr2B 91.169 419 10 12 2523 2920 296005334 296005746 9.790000e-151 544.0
4 TraesCS2A01G231600 chr2B 100.000 38 0 0 746 783 296002104 296002141 2.000000e-08 71.3
5 TraesCS2A01G231600 chr2D 93.475 1410 55 9 1 1387 226529149 226530544 0.000000e+00 2060.0
6 TraesCS2A01G231600 chr2D 96.555 987 26 4 1386 2368 226530627 226531609 0.000000e+00 1628.0
7 TraesCS2A01G231600 chr2D 97.005 768 16 3 3245 4007 226532367 226533132 0.000000e+00 1284.0
8 TraesCS2A01G231600 chr2D 96.496 685 17 2 2523 3201 226531685 226532368 0.000000e+00 1125.0
9 TraesCS2A01G231600 chr6D 89.718 603 45 5 5 600 324828042 324827450 0.000000e+00 754.0
10 TraesCS2A01G231600 chr6B 86.386 617 64 8 1 598 155467142 155467757 0.000000e+00 656.0
11 TraesCS2A01G231600 chr7B 86.460 613 56 13 1 593 123735319 123734714 0.000000e+00 647.0
12 TraesCS2A01G231600 chr4B 87.640 356 35 8 1 348 5708328 5707974 4.820000e-109 405.0
13 TraesCS2A01G231600 chr4B 94.444 90 5 0 643 732 358895013 358894924 5.400000e-29 139.0
14 TraesCS2A01G231600 chr1D 96.552 87 3 0 642 728 227732992 227733078 1.160000e-30 145.0
15 TraesCS2A01G231600 chr1D 95.402 87 4 0 642 728 208396272 208396186 5.400000e-29 139.0
16 TraesCS2A01G231600 chr5D 89.908 109 11 0 643 751 242378736 242378844 1.500000e-29 141.0
17 TraesCS2A01G231600 chr7D 89.855 69 6 1 640 708 191560283 191560350 1.980000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G231600 chr2A 271909172 271913178 4006 True 7400.00 7400 100.000000 1 4007 1 chr2A.!!$R1 4006
1 TraesCS2A01G231600 chr2B 296012709 296013776 1067 False 1570.00 1570 93.151000 2925 4007 1 chr2B.!!$F1 1082
2 TraesCS2A01G231600 chr2B 296002104 296005746 3642 False 977.10 2316 94.623667 746 2920 3 chr2B.!!$F2 2174
3 TraesCS2A01G231600 chr2D 226529149 226533132 3983 False 1524.25 2060 95.882750 1 4007 4 chr2D.!!$F1 4006
4 TraesCS2A01G231600 chr6D 324827450 324828042 592 True 754.00 754 89.718000 5 600 1 chr6D.!!$R1 595
5 TraesCS2A01G231600 chr6B 155467142 155467757 615 False 656.00 656 86.386000 1 598 1 chr6B.!!$F1 597
6 TraesCS2A01G231600 chr7B 123734714 123735319 605 True 647.00 647 86.460000 1 593 1 chr7B.!!$R1 592

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
622 668 0.100861 CGAGCCTTCGTAGTCCCTTC 59.899 60.0 0.0 0.0 41.84 3.46 F
2415 4059 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.0 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 4081 0.111310 CACACACGCACACACATACG 60.111 55.0 0.0 0.0 0.00 3.06 R
3285 4990 1.372087 GCATTCTTGCCTCGGACTGG 61.372 60.0 0.0 0.0 43.38 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 128 2.363147 GGAGGAGAGCCGTCACCT 60.363 66.667 0.00 0.00 45.74 4.00
482 510 2.122099 ACCTTCCCCAGAACCGGT 60.122 61.111 0.00 0.00 0.00 5.28
505 545 4.951963 CTTCGCCGGCGGATCCTC 62.952 72.222 44.95 10.68 40.25 3.71
514 554 3.147595 CGGATCCTCTGGTGGCGA 61.148 66.667 10.75 0.00 0.00 5.54
523 563 2.994995 TGGTGGCGACGAGGTGAT 60.995 61.111 0.00 0.00 0.00 3.06
622 668 0.100861 CGAGCCTTCGTAGTCCCTTC 59.899 60.000 0.00 0.00 41.84 3.46
627 673 3.385111 AGCCTTCGTAGTCCCTTCTTATG 59.615 47.826 0.00 0.00 0.00 1.90
629 675 4.737055 GCCTTCGTAGTCCCTTCTTATGAC 60.737 50.000 0.00 0.00 0.00 3.06
636 682 2.166664 GTCCCTTCTTATGACGAGTGCT 59.833 50.000 0.00 0.00 0.00 4.40
641 687 3.006112 TCTTATGACGAGTGCTCCTCT 57.994 47.619 0.00 0.00 38.11 3.69
703 749 9.599866 AAATTGTAATGATTCTCACAGACGATA 57.400 29.630 0.00 0.00 0.00 2.92
706 752 9.678941 TTGTAATGATTCTCACAGACGATATAC 57.321 33.333 0.00 0.00 0.00 1.47
716 762 8.692710 TCTCACAGACGATATACTGGTTATTTT 58.307 33.333 0.00 0.00 38.30 1.82
1194 2730 2.123854 TCTCCACGGGGATCCTCG 60.124 66.667 32.45 32.45 43.91 4.63
1614 3248 7.515215 CGAGTGTCCGTGATCTGTAAATAAATG 60.515 40.741 0.00 0.00 0.00 2.32
1742 3376 3.640407 GAGCCCTGCCACTCCACA 61.640 66.667 0.00 0.00 0.00 4.17
1860 3494 5.392380 GGTTCACTTCCATGCTCACAAATAG 60.392 44.000 0.00 0.00 0.00 1.73
1861 3495 4.910195 TCACTTCCATGCTCACAAATAGT 58.090 39.130 0.00 0.00 0.00 2.12
1862 3496 6.048732 TCACTTCCATGCTCACAAATAGTA 57.951 37.500 0.00 0.00 0.00 1.82
1863 3497 6.653020 TCACTTCCATGCTCACAAATAGTAT 58.347 36.000 0.00 0.00 0.00 2.12
2099 3739 1.926490 CGTGCTTGCCAAAACTTGC 59.074 52.632 0.00 0.00 0.00 4.01
2102 3742 0.527385 TGCTTGCCAAAACTTGCGTC 60.527 50.000 0.00 0.00 0.00 5.19
2142 3782 1.078567 CTGAGGCTGAGCTTGACCC 60.079 63.158 3.72 0.00 0.00 4.46
2193 3833 1.228583 TCTGGTGAGCTCCGTGTCT 60.229 57.895 12.15 0.00 0.00 3.41
2266 3906 2.521451 TTTAGCCCCACGCAGACCA 61.521 57.895 0.00 0.00 41.38 4.02
2373 4017 4.213694 CCTGAGATAAGAGTTCATGCATGC 59.786 45.833 22.25 11.82 0.00 4.06
2408 4052 4.678509 AAACTACTTGTGTGTGTGTGTG 57.321 40.909 0.00 0.00 0.00 3.82
2410 4054 3.000041 ACTACTTGTGTGTGTGTGTGTG 59.000 45.455 0.00 0.00 0.00 3.82
2412 4056 1.535028 ACTTGTGTGTGTGTGTGTGTG 59.465 47.619 0.00 0.00 0.00 3.82
2414 4058 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2415 4059 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
2416 4060 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
2417 4061 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
2418 4062 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
2445 4089 2.740826 GCGTGTGGGCGTATGTGT 60.741 61.111 0.00 0.00 0.00 3.72
2446 4090 3.022401 GCGTGTGGGCGTATGTGTG 62.022 63.158 0.00 0.00 0.00 3.82
2447 4091 1.666553 CGTGTGGGCGTATGTGTGT 60.667 57.895 0.00 0.00 0.00 3.72
2448 4092 1.866237 GTGTGGGCGTATGTGTGTG 59.134 57.895 0.00 0.00 0.00 3.82
2449 4093 1.963855 TGTGGGCGTATGTGTGTGC 60.964 57.895 0.00 0.00 0.00 4.57
2450 4094 2.740440 TGGGCGTATGTGTGTGCG 60.740 61.111 0.00 0.00 0.00 5.34
2451 4095 2.740826 GGGCGTATGTGTGTGCGT 60.741 61.111 0.00 0.00 0.00 5.24
2452 4096 2.474266 GGCGTATGTGTGTGCGTG 59.526 61.111 0.00 0.00 0.00 5.34
2453 4097 2.314647 GGCGTATGTGTGTGCGTGT 61.315 57.895 0.00 0.00 0.00 4.49
2454 4098 1.154672 GCGTATGTGTGTGCGTGTG 60.155 57.895 0.00 0.00 0.00 3.82
2455 4099 1.827315 GCGTATGTGTGTGCGTGTGT 61.827 55.000 0.00 0.00 0.00 3.72
2456 4100 0.111310 CGTATGTGTGTGCGTGTGTG 60.111 55.000 0.00 0.00 0.00 3.82
2457 4101 0.934496 GTATGTGTGTGCGTGTGTGT 59.066 50.000 0.00 0.00 0.00 3.72
2458 4102 0.933796 TATGTGTGTGCGTGTGTGTG 59.066 50.000 0.00 0.00 0.00 3.82
2459 4103 1.024046 ATGTGTGTGCGTGTGTGTGT 61.024 50.000 0.00 0.00 0.00 3.72
2460 4104 1.225991 GTGTGTGCGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2461 4105 1.669437 TGTGTGCGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2462 4106 1.225991 GTGTGCGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2463 4107 1.669437 TGTGCGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2464 4108 1.225991 GTGCGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2465 4109 1.669437 TGCGTGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2466 4110 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2467 4111 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
2468 4112 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2469 4113 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2470 4114 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2471 4115 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2472 4116 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2473 4117 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2474 4118 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2475 4119 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2476 4120 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2477 4121 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2478 4122 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2479 4123 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2480 4124 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2481 4125 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2482 4126 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2483 4127 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2484 4128 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2485 4129 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2486 4130 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
2501 4145 3.072330 TGTGTGTCATTGGGAAAGCTAGA 59.928 43.478 0.00 0.00 0.00 2.43
2502 4146 3.686726 GTGTGTCATTGGGAAAGCTAGAG 59.313 47.826 0.00 0.00 0.00 2.43
2504 4148 3.935828 GTGTCATTGGGAAAGCTAGAGTC 59.064 47.826 0.00 0.00 0.00 3.36
2505 4149 3.840666 TGTCATTGGGAAAGCTAGAGTCT 59.159 43.478 0.00 0.00 0.00 3.24
2507 4151 5.105310 TGTCATTGGGAAAGCTAGAGTCTAC 60.105 44.000 0.00 0.00 0.00 2.59
2509 4153 4.803098 TTGGGAAAGCTAGAGTCTACAC 57.197 45.455 0.00 0.00 0.00 2.90
2511 4155 4.157246 TGGGAAAGCTAGAGTCTACACAA 58.843 43.478 0.00 0.00 0.00 3.33
2512 4156 4.591498 TGGGAAAGCTAGAGTCTACACAAA 59.409 41.667 0.00 0.00 0.00 2.83
2513 4157 5.248477 TGGGAAAGCTAGAGTCTACACAAAT 59.752 40.000 0.00 0.00 0.00 2.32
2514 4158 5.582665 GGGAAAGCTAGAGTCTACACAAATG 59.417 44.000 0.00 0.00 0.00 2.32
2549 4234 7.280652 AGACAATTTTCTTGGGTTTTCATGTTG 59.719 33.333 0.00 0.00 0.00 3.33
3095 4800 7.625828 ACAGGTTAAAAGTGGCTATCATAAC 57.374 36.000 0.00 0.00 0.00 1.89
3144 4849 7.432869 CAAAATTGTCTGTTTACTGAATGGGA 58.567 34.615 0.00 0.00 0.00 4.37
3184 4889 4.214986 TCGACTAAAATCCCAGCATTCA 57.785 40.909 0.00 0.00 0.00 2.57
3217 4922 6.757897 CAAAGGGAATTTGCTGATACAGTA 57.242 37.500 0.00 0.00 41.77 2.74
3219 4924 5.435686 AGGGAATTTGCTGATACAGTACA 57.564 39.130 0.00 0.00 33.43 2.90
3233 4938 6.551227 TGATACAGTACACTCCTGCAGATTAT 59.449 38.462 17.39 0.00 33.09 1.28
3285 4990 7.190871 TGAACAAATCAACGTAAGGTTTTCTC 58.809 34.615 0.00 0.00 36.49 2.87
3378 5086 0.325484 CCCTGGGAAATGGAATGGCA 60.325 55.000 7.01 0.00 0.00 4.92
3535 5252 7.941238 ACACTAAGGATATAGCTACCTACGAAA 59.059 37.037 0.00 0.00 33.34 3.46
3615 5336 5.375417 TGTTATCAACTTCTGCATGGTTG 57.625 39.130 15.72 15.72 40.87 3.77
3640 5361 6.625300 GCGATACTTAACCTGATCCATATCGT 60.625 42.308 10.82 0.00 41.22 3.73
3698 5419 3.209410 AGATTTGATTCATCCAGCCGAC 58.791 45.455 0.00 0.00 0.00 4.79
3742 5463 4.536090 TCTTCTCTTTGGCTTCCTCCAATA 59.464 41.667 0.00 0.00 44.78 1.90
3985 5706 4.811969 TCCTAAAGACGATGCCAGTTAA 57.188 40.909 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.449967 TAGGGGTTCAGACTGGCCGA 62.450 60.000 1.81 0.00 0.00 5.54
101 103 3.456365 GCTCTCCTCCTCGCAGCA 61.456 66.667 0.00 0.00 0.00 4.41
138 140 2.754658 CACCGGCGTCTACCTCCT 60.755 66.667 6.01 0.00 0.00 3.69
382 403 2.663188 GCTCCATGGCGTCGATCC 60.663 66.667 6.96 0.00 0.00 3.36
495 535 4.554036 GCCACCAGAGGATCCGCC 62.554 72.222 12.40 5.46 33.66 6.13
496 536 4.899239 CGCCACCAGAGGATCCGC 62.899 72.222 7.52 7.52 33.66 5.54
497 537 3.147595 TCGCCACCAGAGGATCCG 61.148 66.667 5.98 0.00 33.66 4.18
498 538 2.501610 GTCGCCACCAGAGGATCC 59.498 66.667 2.48 2.48 33.66 3.36
499 539 2.105128 CGTCGCCACCAGAGGATC 59.895 66.667 0.00 0.00 0.00 3.36
500 540 2.362503 TCGTCGCCACCAGAGGAT 60.363 61.111 0.00 0.00 0.00 3.24
501 541 3.062466 CTCGTCGCCACCAGAGGA 61.062 66.667 0.00 0.00 0.00 3.71
502 542 4.135153 CCTCGTCGCCACCAGAGG 62.135 72.222 0.00 0.00 43.43 3.69
503 543 3.374402 ACCTCGTCGCCACCAGAG 61.374 66.667 0.00 0.00 0.00 3.35
504 544 3.680786 CACCTCGTCGCCACCAGA 61.681 66.667 0.00 0.00 0.00 3.86
505 545 3.006756 ATCACCTCGTCGCCACCAG 62.007 63.158 0.00 0.00 0.00 4.00
506 546 2.994995 ATCACCTCGTCGCCACCA 60.995 61.111 0.00 0.00 0.00 4.17
514 554 1.995626 CCCCTTCCCATCACCTCGT 60.996 63.158 0.00 0.00 0.00 4.18
558 604 4.770874 CGGCGACACGGGGGAAAT 62.771 66.667 0.00 0.00 0.00 2.17
602 648 1.321074 AAGGGACTACGAAGGCTCGG 61.321 60.000 10.29 0.00 45.05 4.63
636 682 1.550524 CAATCCGAGGTCACAAGAGGA 59.449 52.381 0.00 0.00 0.00 3.71
641 687 2.158740 TCAAACCAATCCGAGGTCACAA 60.159 45.455 0.00 0.00 38.76 3.33
880 2416 1.440850 CGTTCGTGGTGCATGCAAG 60.441 57.895 24.58 14.18 0.00 4.01
1106 2642 0.744414 GCGTCAGCACCACCATGTAT 60.744 55.000 0.00 0.00 44.35 2.29
1194 2730 4.491409 GAGGGCGAAAGGGAGGGC 62.491 72.222 0.00 0.00 0.00 5.19
1579 3213 3.386237 GGACACTCGCTGCCCTCT 61.386 66.667 0.00 0.00 0.00 3.69
1614 3248 7.556635 ACCCTCTCAAACCTACAATTTATTAGC 59.443 37.037 0.00 0.00 0.00 3.09
1782 3416 4.729918 CCCAGGAGGCACAGGCAC 62.730 72.222 0.00 0.00 43.71 5.01
2037 3677 1.788229 TATTCCGGTGCTGATCTGGA 58.212 50.000 0.00 0.00 38.42 3.86
2099 3739 0.179156 GCATGGTGGCTCATTTGACG 60.179 55.000 0.00 0.00 0.00 4.35
2102 3742 1.140161 CCGCATGGTGGCTCATTTG 59.860 57.895 0.00 0.00 0.00 2.32
2193 3833 2.429250 CACCCACGTCTGGTACATGATA 59.571 50.000 0.00 0.00 38.20 2.15
2217 3857 1.301293 CACAGGCCCCTTCTTCTCC 59.699 63.158 0.00 0.00 0.00 3.71
2266 3906 1.408822 GGAGAAGATTGCGGAACCCAT 60.409 52.381 0.00 0.00 0.00 4.00
2389 4033 3.000041 CACACACACACACACAAGTAGT 59.000 45.455 0.00 0.00 0.00 2.73
2390 4034 3.000041 ACACACACACACACACAAGTAG 59.000 45.455 0.00 0.00 0.00 2.57
2393 4037 1.535028 ACACACACACACACACACAAG 59.465 47.619 0.00 0.00 0.00 3.16
2394 4038 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
2396 4040 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
2398 4042 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2400 4044 2.277247 GCGCACACACACACACAC 60.277 61.111 0.30 0.00 0.00 3.82
2428 4072 2.740826 ACACATACGCCCACACGC 60.741 61.111 0.00 0.00 36.19 5.34
2429 4073 1.666553 ACACACATACGCCCACACG 60.667 57.895 0.00 0.00 39.50 4.49
2430 4074 1.866237 CACACACATACGCCCACAC 59.134 57.895 0.00 0.00 0.00 3.82
2431 4075 1.963855 GCACACACATACGCCCACA 60.964 57.895 0.00 0.00 0.00 4.17
2432 4076 2.867472 GCACACACATACGCCCAC 59.133 61.111 0.00 0.00 0.00 4.61
2433 4077 2.740440 CGCACACACATACGCCCA 60.740 61.111 0.00 0.00 0.00 5.36
2434 4078 2.740826 ACGCACACACATACGCCC 60.741 61.111 0.00 0.00 0.00 6.13
2436 4080 1.154672 CACACGCACACACATACGC 60.155 57.895 0.00 0.00 0.00 4.42
2437 4081 0.111310 CACACACGCACACACATACG 60.111 55.000 0.00 0.00 0.00 3.06
2438 4082 0.934496 ACACACACGCACACACATAC 59.066 50.000 0.00 0.00 0.00 2.39
2439 4083 0.933796 CACACACACGCACACACATA 59.066 50.000 0.00 0.00 0.00 2.29
2441 4085 1.669437 ACACACACACGCACACACA 60.669 52.632 0.00 0.00 0.00 3.72
2442 4086 1.225991 CACACACACACGCACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2443 4087 1.669437 ACACACACACACGCACACA 60.669 52.632 0.00 0.00 0.00 3.72
2444 4088 1.225991 CACACACACACACGCACAC 60.226 57.895 0.00 0.00 0.00 3.82
2445 4089 1.669437 ACACACACACACACGCACA 60.669 52.632 0.00 0.00 0.00 4.57
2446 4090 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
2447 4091 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
2448 4092 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
2449 4093 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
2450 4094 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2451 4095 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2452 4096 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2453 4097 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2454 4098 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2455 4099 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2456 4100 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2457 4101 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2458 4102 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2459 4103 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2460 4104 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2461 4105 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2462 4106 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2463 4107 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2464 4108 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2465 4109 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2466 4110 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2467 4111 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
2468 4112 1.152510 TGACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
2469 4113 2.106477 ATGACACACACACACACACA 57.894 45.000 0.00 0.00 0.00 3.72
2470 4114 2.477694 CCAATGACACACACACACACAC 60.478 50.000 0.00 0.00 0.00 3.82
2471 4115 1.742268 CCAATGACACACACACACACA 59.258 47.619 0.00 0.00 0.00 3.72
2472 4116 1.065401 CCCAATGACACACACACACAC 59.935 52.381 0.00 0.00 0.00 3.82
2473 4117 1.065126 TCCCAATGACACACACACACA 60.065 47.619 0.00 0.00 0.00 3.72
2474 4118 1.674359 TCCCAATGACACACACACAC 58.326 50.000 0.00 0.00 0.00 3.82
2475 4119 2.426842 TTCCCAATGACACACACACA 57.573 45.000 0.00 0.00 0.00 3.72
2476 4120 2.543653 GCTTTCCCAATGACACACACAC 60.544 50.000 0.00 0.00 0.00 3.82
2477 4121 1.680735 GCTTTCCCAATGACACACACA 59.319 47.619 0.00 0.00 0.00 3.72
2478 4122 1.956477 AGCTTTCCCAATGACACACAC 59.044 47.619 0.00 0.00 0.00 3.82
2479 4123 2.363306 AGCTTTCCCAATGACACACA 57.637 45.000 0.00 0.00 0.00 3.72
2480 4124 3.674997 TCTAGCTTTCCCAATGACACAC 58.325 45.455 0.00 0.00 0.00 3.82
2481 4125 3.327757 ACTCTAGCTTTCCCAATGACACA 59.672 43.478 0.00 0.00 0.00 3.72
2482 4126 3.935828 GACTCTAGCTTTCCCAATGACAC 59.064 47.826 0.00 0.00 0.00 3.67
2483 4127 3.840666 AGACTCTAGCTTTCCCAATGACA 59.159 43.478 0.00 0.00 0.00 3.58
2484 4128 4.479786 AGACTCTAGCTTTCCCAATGAC 57.520 45.455 0.00 0.00 0.00 3.06
2485 4129 5.023452 TGTAGACTCTAGCTTTCCCAATGA 58.977 41.667 0.00 0.00 0.00 2.57
2486 4130 5.112686 GTGTAGACTCTAGCTTTCCCAATG 58.887 45.833 0.00 0.00 0.00 2.82
2501 4145 5.542635 TCTCAGGGTTACATTTGTGTAGACT 59.457 40.000 0.00 0.00 0.00 3.24
2502 4146 5.638234 GTCTCAGGGTTACATTTGTGTAGAC 59.362 44.000 0.00 0.00 0.00 2.59
2504 4148 5.547465 TGTCTCAGGGTTACATTTGTGTAG 58.453 41.667 0.00 0.00 0.00 2.74
2505 4149 5.554437 TGTCTCAGGGTTACATTTGTGTA 57.446 39.130 0.00 0.00 0.00 2.90
2507 4151 5.964958 ATTGTCTCAGGGTTACATTTGTG 57.035 39.130 0.00 0.00 0.00 3.33
2509 4153 7.661040 AGAAAATTGTCTCAGGGTTACATTTG 58.339 34.615 0.00 0.00 0.00 2.32
2511 4155 7.255942 CCAAGAAAATTGTCTCAGGGTTACATT 60.256 37.037 0.00 0.00 0.00 2.71
2512 4156 6.209391 CCAAGAAAATTGTCTCAGGGTTACAT 59.791 38.462 0.00 0.00 0.00 2.29
2513 4157 5.534654 CCAAGAAAATTGTCTCAGGGTTACA 59.465 40.000 0.00 0.00 0.00 2.41
2514 4158 5.048013 CCCAAGAAAATTGTCTCAGGGTTAC 60.048 44.000 20.74 0.00 37.77 2.50
2549 4234 1.133668 AGCCTATTCCTTGCCATGGAC 60.134 52.381 18.40 7.64 32.65 4.02
2907 4612 4.617995 GCAACTTGCATGTGCTTGGTATTA 60.618 41.667 8.97 0.00 44.26 0.98
2980 4685 7.928307 TTCAGCAAGCTATTTATCTGTTTCT 57.072 32.000 0.00 0.00 0.00 2.52
3011 4716 6.959639 TGAAGGAAGCATTTGTTTAGACTT 57.040 33.333 0.00 0.00 0.00 3.01
3095 4800 1.033574 GGGGACTGATACCAGACTCG 58.966 60.000 0.00 0.00 43.02 4.18
3144 4849 5.694910 AGTCGATGAATTCTTTGTGTACGTT 59.305 36.000 7.05 0.00 0.00 3.99
3184 4889 5.671742 CAAATTCCCTTTGCAAATTCGTT 57.328 34.783 13.23 2.08 37.98 3.85
3207 4912 3.696548 TCTGCAGGAGTGTACTGTATCAG 59.303 47.826 15.13 0.00 38.22 2.90
3217 4922 6.893583 ACTGATTTATAATCTGCAGGAGTGT 58.106 36.000 15.13 1.17 0.00 3.55
3219 4924 7.129457 TGACTGATTTATAATCTGCAGGAGT 57.871 36.000 15.13 2.57 0.00 3.85
3285 4990 1.372087 GCATTCTTGCCTCGGACTGG 61.372 60.000 0.00 0.00 43.38 4.00
3345 5053 4.002006 AGGGTTCCTGGTTCTGCA 57.998 55.556 0.00 0.00 29.57 4.41
3378 5086 4.651503 ACCGGAATAGACAACATCAGAGAT 59.348 41.667 9.46 0.00 0.00 2.75
3535 5252 6.839124 TGTTTGTAGCAGATGATTCCAAAT 57.161 33.333 0.00 0.00 0.00 2.32
3615 5336 5.744345 CGATATGGATCAGGTTAAGTATCGC 59.256 44.000 0.00 0.00 35.11 4.58
3640 5361 1.557371 TGGTGGTATTTGGATCTGCGA 59.443 47.619 0.00 0.00 0.00 5.10
3698 5419 5.238583 AGAACGACTTGATTACCTTGAAGG 58.761 41.667 10.24 10.24 42.49 3.46
3742 5463 6.039382 GTGTTCAATTTCAGGTAGGTGAACTT 59.961 38.462 13.61 0.00 43.25 2.66
3893 5614 3.571401 GGCAATGGATCTATTGGTTCCTG 59.429 47.826 27.12 7.03 38.25 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.